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Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3

Nature Structural & Molecular Biology volume 17, pages 1241–1246 (2010)Cite this article

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Abstract

The toxin colicin E3 targets the 30S subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. We present the crystal structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase). The structure reveals how the rRNase domain of colicin binds to the A site of the decoding center in the 70S ribosome and cleaves the 16S ribosomal RNA (rRNA) between A1493 and G1494. The cleavage mechanism involves the concerted action of conserved residues Glu62 and His58 of the cytotoxic domain of colicin E3. These residues activate the 16S rRNA for 2′ OH–induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function.

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Figure 1: Structure of E3-rRNase bound to the 70S ribosome.
Figure 2: A mechanism for 16S rRNA cleavage by E3-rRNase.
Figure 3: The N terminus of E3-rRNase contacts ribosomal protein S12.
Figure 4: Conformational changes at helix 69 of 23S rRNA induced by E3-rRNase binding and cleavage.

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Acknowledgements

We would like to thank C. Neubauer, I.S. Fernandez, Y. Gao, M. Schmeing, J. Li and M. Ortiz-Lombardia for helpful discussions and N. Kirkpatrick for technical assistance. V.R. was supported by the Medical Research Council (UK), the Wellcome Trust, the Louis-Jeantet Foundation and the Agouron Institute. C.K. acknowledges the Biotechnology and Biological Sciences Research Councils (UK) for funding.

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  1. C Leong Ng and Kathrin Lang: These authors contributed equally to this work.

Authors and Affiliations

  1. MRC Laboratory of Molecular Biology, Cambridge, UK

    C Leong Ng, Kathrin Lang, Ann C Kelley & V Ramakrishnan

  2. Department of Biology, University of York, York, UK

    Nicola A G Meenan, Amit Sharma & Colin Kleanthous

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  1. C Leong Ng
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Contributions

C.L.N. and K.L. carried out the crystallographic and biochemical experiments, analyzed data and interpreted results; N.A.G.M. and A.S. expressed and purified the E3-rRNase mutants; A.C.K. prepared 70S ribosomes; C.K. and V.R. supervised the research; K.L., C.L.N., C.K. and V.R. wrote the paper.

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Correspondence to Colin Kleanthous or V Ramakrishnan.

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Ng, C., Lang, K., Meenan, N. et al. Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3. Nat Struct Mol Biol 17, 1241–1246 (2010). https://doi.org/10.1038/nsmb.1896

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